Mutations and Horizontal Gene Transfer

Question 1

Proofreading Enzymes

Answer 1

Enzymes that can back up and excise a nucleotide not properly hydrogen bonded to the opposing nucleobase in the template strand

Question 2

Mismatch Repair - Function

Answer 2

Fixes errors missed by the proofreading of DNA polymerases

Question 3

Mismatch Repair - Steps

Answer 3

1 Protein binds to the mismatched nucleobase
2. enzyme cuts the sugar-phosphate backbone
3. enzyme degrades that region of the DNA strand
4. DNA polymerase and ligase adds correct nucleobases to the DNA strand

Question 4

How does the enzyme know which strand is the strand with the base error?

Answer 4

Template strands are old and therefore have been methylated but newly created replica strands are not methylated after they are first made and that allows the new enzyme to know which strand has the base error

Question 5

Base Excision Repair - Function

Answer 5

Fixes nucleobases that have been damaged or oxidized

Question 6

Base Excision Repair - Steps

Answer 6

1. DNA glycosylase removes the damaged nucleobase from the sugar-phosphate backbone
2. Enzyme recognizes the missing nucleobase and cuts the strand at that site
3. DNA polymerase and ligase repairs and fills the strand of DNA

Question 7

Photoreactivation

Answer 7

relies on an enzyme that uses the energy gained from visible light to break the thymine dimer covalent bonds

Question 8

What are the methods to repair thymine dimers?

Answer 8

Photoreactivation and Nucleotide excision repair

Question 9

What is the difference between nucleotide excision repair and base excision repair?

Answer 9

Nucleotide excision repair repairs helix-distorting lesions while Base excision repair repairs non/minimal helix distorting lesions

Question 10

SOS Repair - Function

Answer 10

Bacteria Only

Last-effort attempt to repair extensively damaged DNA. Repairs DNA that is too damaged to be repaired by other repair mechanisms

Question 11

What is the main flaw in SOS repair?

Answer 11

SOS DNA Polymerase has no proofreading ability and will continue to make errors in the repair attempt

Question 12

SOS Mutagenesis

Answer 12

Errors made as a result of SOS DNA Polymerase errors/non-proofreading

Question 13

Insertional inactivation

Answer 13

Transposons disrupts the function of the gene

Question 14

Base Analogs

Answer 14

Molecules that structurally resemble nucleobases but have different hydrogen-bonding properties

Question 15

Intercalating Agents

Answer 15

Flat molecules that intercalate between adjacent bases of DNA and pushes nucleotides apart thereby increasing the chance that insertions or deletions will be made during DNA replication

Question 16

UV Radiation Muatations

Answer 16

Causes covalent bonds to form between adjacent thymine nucleobases and thereby promoting thymine dimers

Question 17

X-Ray induced Mutations

Answer 17

Single- and double- strand breaks in DNA
Changes to nucleobases
Double-strand breaks often result in deletions that are lethal to the cell

Question 18

What are the 3 methods of Horizontal Gene Transfer

Answer 18

Bacterial Transformation
Transduction
Conjugation

Question 19

Bacterial Transformation

Answer 19

When “naked” DNA is taken up from the environment into the cell

Question 20

Transduction

Answer 20

DNA is transferred from one bacterial cell to another via bacteriophage

Question 21

Conjugation

Answer 21

DNA transferred during cell-to-cell contact

Question 22

Replicon

Answer 22

When transferred DNA has a origin of replication

Question 23

Homologous Recombination

Answer 23

When a chromosomal fragment is transferred, it then must become integrated into a replicon to be maintained in a population

Question 24

Types of replicons

Answer 24

Plasmids and Chromosomes

Question 25

Types of non-replicons

Answer 25

Fragments of chromosomal DNA

Question 26

What is the origin of “naked DNA”

Answer 26

Lysed Cells whose chromosomes break up into many smaller pieces

Question 27

What is DNase?

Answer 27

an enzyme that degrades DNA

Question 28

Competence

Answer 28

a state that allows a cell to take up DNA

Question 29

What are the steps of Bacterial Transformation?

Answer 29

1. donor dsDNA binds to a extracellular receptor on competent cell
2. one strand of dsDNA enters the cell, complement stand degrades
3. homologous recombination integrates donor cell into recipient’s genome, replaced strand is degraded
4. Since only one strand contains the donor DNA, only one of the daughter cells will contain the mutant genome, the other will remain the same as the parent

Question 30

Plasmid Transfer - Method

Answer 30

Most frequently transferred to other cells via conjugation

Question 31

Conjugative plasmids

Answer 31

Direct their own transfer from donor to recipient cells

Question 32

F Plasmid

Answer 32

Fertility plasmid of E. Coli